Added RcppArmadillo backend for BLAS-optimized bulk affinity and distance matrix computation, replacing per-element R loops
Scalar affinity function for clone/mutate hot path avoids 1x1 matrix allocation overhead
C++ implementations for clonal selection iteration, network suppression, kmeans++ initialization, final assignment, somatic hypermutation (5 methods), and idiotypic network dynamics
R6 Class Architecture
New ImmuneRepertoire class for antibody collections with metadata tracking (isotype, state, age, lineage)
New ImmuneAlgorithm abstract base class with fit/predict/summary interface
New AINet class wrapping core algorithm with composable module injection
Both R6 composition and functional API equally supported
New Modules
SHMEngine — Five somatic hypermutation strategies: uniform (original behavior), airs (affinity-proportional), hotspot (feature-gradient-weighted), energy (budget-constrained), and adaptive (per-feature Adam-like moment tracking)
IdiotypicNetwork — Antibody-antibody network dynamics with bell-shaped activation function replacing epsilon-threshold suppression
GerminalCenter — T-follicular helper mediated selection with task-aware quality scoring and resource competition
Microenvironment — Density-dependent zone classification (stable/explore/boundary) with chemokine-like gradient computation
VDJLibrary — Combinatorial V(D)J gene library initialization via PCA, k-means clustering, or random partition of feature space
ActivationGate — Two-signal activation gate requiring both antigen recognition and costimulatory context (density, danger, or entropy)
MemoryPool — Archive high-affinity antibodies as long-lived memory cells with threshold-based recall
ClassSwitcher — Isotype class switching (IgM broad, IgG specific, IgA boundary) modulating effective kernel width
ConvergentSelector — Cross-repertoire consensus identification of public antibodies for ensemble methods
